Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs1104856

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3817883 (GRCh38.p13) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.333696 (88326/264690, TOPMED)
G=0.333167 (46706/140188, GnomAD)
G=0.37401 (7065/18890, ALFA) (+ 12 more)
G=0.43765 (7335/16760, 8.3KJPN)
G=0.3097 (1551/5008, 1000G)
G=0.4217 (1889/4480, Estonian)
G=0.4385 (1690/3854, ALSPAC)
G=0.4415 (1637/3708, TWINSUK)
G=0.3433 (1006/2930, KOREAN)
G=0.417 (416/998, GoNL)
G=0.442 (265/600, NorthernSweden)
G=0.227 (109/480, SGDP_PRJ)
G=0.255 (55/216, Qatari)
G=0.278 (59/212, Vietnamese)
G=0.24 (12/50, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CEP104 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p13 chr 1 NC_000001.11:g.3817883G>A
GRCh38.p13 chr 1 NC_000001.11:g.3817883G>C
GRCh37.p13 chr 1 NC_000001.10:g.3734447G>A
GRCh37.p13 chr 1 NC_000001.10:g.3734447G>C
CEP104 RefSeqGene NG_046726.1:g.44351C>T
CEP104 RefSeqGene NG_046726.1:g.44351C>G
Gene: CEP104, centrosomal protein 104 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEP104 transcript NM_014704.4:c.2572-1513C>T N/A Intron Variant
CEP104 transcript variant X2 XM_005244815.4:c.2680-151…

XM_005244815.4:c.2680-1513C>T

N/A Intron Variant
CEP104 transcript variant X3 XM_011542474.3:c.2590-151…

XM_011542474.3:c.2590-1513C>T

N/A Intron Variant
CEP104 transcript variant X7 XM_017002918.2:c.2398-151…

XM_017002918.2:c.2398-1513C>T

N/A Intron Variant
CEP104 transcript variant X8 XM_017002919.2:c.2374-151…

XM_017002919.2:c.2374-1513C>T

N/A Intron Variant
CEP104 transcript variant X1 XM_024451101.1:c.2698-151…

XM_024451101.1:c.2698-1513C>T

N/A Intron Variant
CEP104 transcript variant X4 XM_024451102.1:c.2524-151…

XM_024451102.1:c.2524-1513C>T

N/A Intron Variant
CEP104 transcript variant X5 XM_024451103.1:c.2506-151…

XM_024451103.1:c.2506-1513C>T

N/A Intron Variant
CEP104 transcript variant X6 XM_024451104.1:c.2500-151…

XM_024451104.1:c.2500-1513C>T

N/A Intron Variant
CEP104 transcript variant X9 XM_024451106.1:c.2326-151…

XM_024451106.1:c.2326-1513C>T

N/A Intron Variant
CEP104 transcript variant X10 XM_024451108.1:c. N/A Genic Downstream Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 G=0.37401 A=0.62599
European Sub 14286 G=0.42636 A=0.57364
African Sub 2946 G=0.1280 A=0.8720
African Others Sub 114 G=0.053 A=0.947
African American Sub 2832 G=0.1310 A=0.8690
Asian Sub 112 G=0.339 A=0.661
East Asian Sub 86 G=0.29 A=0.71
Other Asian Sub 26 G=0.50 A=0.50
Latin American 1 Sub 146 G=0.301 A=0.699
Latin American 2 Sub 610 G=0.407 A=0.593
South Asian Sub 98 G=0.24 A=0.76
Other Sub 692 G=0.351 A=0.649


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.333696 A=0.666304
gnomAD - Genomes Global Study-wide 140188 G=0.333167 A=0.666833
gnomAD - Genomes European Sub 75886 G=0.41927 A=0.58073
gnomAD - Genomes African Sub 42046 G=0.13797 A=0.86203
gnomAD - Genomes American Sub 13658 G=0.45197 A=0.54803
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.3474 A=0.6526
gnomAD - Genomes East Asian Sub 3126 G=0.3193 A=0.6807
gnomAD - Genomes Other Sub 2150 G=0.3549 A=0.6451
Allele Frequency Aggregator Total Global 18890 G=0.37401 A=0.62599
Allele Frequency Aggregator European Sub 14286 G=0.42636 A=0.57364
Allele Frequency Aggregator African Sub 2946 G=0.1280 A=0.8720
Allele Frequency Aggregator Other Sub 692 G=0.351 A=0.649
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.407 A=0.593
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.301 A=0.699
Allele Frequency Aggregator Asian Sub 112 G=0.339 A=0.661
Allele Frequency Aggregator South Asian Sub 98 G=0.24 A=0.76
8.3KJPN JAPANESE Study-wide 16760 G=0.43765 A=0.56235
1000Genomes Global Study-wide 5008 G=0.3097 A=0.6903
1000Genomes African Sub 1322 G=0.0847 A=0.9153
1000Genomes East Asian Sub 1008 G=0.3383 A=0.6617
1000Genomes Europe Sub 1006 G=0.4294 A=0.5706
1000Genomes South Asian Sub 978 G=0.332 A=0.668
1000Genomes American Sub 694 G=0.491 A=0.509
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.4217 A=0.5783
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.4385 A=0.5615
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.4415 A=0.5585
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.3433 A=0.6567, C=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.417 A=0.583
Northern Sweden ACPOP Study-wide 600 G=0.442 A=0.558
SGDP_PRJ Global Study-wide 480 G=0.227 A=0.773
Qatari Global Study-wide 216 G=0.255 A=0.745
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.278 A=0.722
Siberian Global Study-wide 50 G=0.24 A=0.76
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement G= A C
GRCh38.p13 chr 1 NC_000001.11:g.3817883= NC_000001.11:g.3817883G>A NC_000001.11:g.3817883G>C
GRCh37.p13 chr 1 NC_000001.10:g.3734447= NC_000001.10:g.3734447G>A NC_000001.10:g.3734447G>C
CEP104 RefSeqGene NG_046726.1:g.44351= NG_046726.1:g.44351C>T NG_046726.1:g.44351C>G
CEP104 transcript NM_014704.3:c.2572-1513= NM_014704.3:c.2572-1513C>T NM_014704.3:c.2572-1513C>G
CEP104 transcript NM_014704.4:c.2572-1513= NM_014704.4:c.2572-1513C>T NM_014704.4:c.2572-1513C>G
CEP104 transcript variant X1 XM_005244815.1:c.2680-1513= XM_005244815.1:c.2680-1513C>T XM_005244815.1:c.2680-1513C>G
CEP104 transcript variant X2 XM_005244815.4:c.2680-1513= XM_005244815.4:c.2680-1513C>T XM_005244815.4:c.2680-1513C>G
CEP104 transcript variant X3 XM_011542474.3:c.2590-1513= XM_011542474.3:c.2590-1513C>T XM_011542474.3:c.2590-1513C>G
CEP104 transcript variant X7 XM_017002918.2:c.2398-1513= XM_017002918.2:c.2398-1513C>T XM_017002918.2:c.2398-1513C>G
CEP104 transcript variant X8 XM_017002919.2:c.2374-1513= XM_017002919.2:c.2374-1513C>T XM_017002919.2:c.2374-1513C>G
CEP104 transcript variant X1 XM_024451101.1:c.2698-1513= XM_024451101.1:c.2698-1513C>T XM_024451101.1:c.2698-1513C>G
CEP104 transcript variant X4 XM_024451102.1:c.2524-1513= XM_024451102.1:c.2524-1513C>T XM_024451102.1:c.2524-1513C>G
CEP104 transcript variant X5 XM_024451103.1:c.2506-1513= XM_024451103.1:c.2506-1513C>T XM_024451103.1:c.2506-1513C>G
CEP104 transcript variant X6 XM_024451104.1:c.2500-1513= XM_024451104.1:c.2500-1513C>T XM_024451104.1:c.2500-1513C>G
CEP104 transcript variant X9 XM_024451106.1:c.2326-1513= XM_024451106.1:c.2326-1513C>T XM_024451106.1:c.2326-1513C>G
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

65 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1289624 Oct 13, 2000 (86)
2 SC_JCM ss5894393 Feb 20, 2003 (111)
3 WI_SSAHASNP ss6396329 Feb 20, 2003 (111)
4 BCM_SSAHASNP ss9897076 Jul 11, 2003 (116)
5 SC_SNP ss12992576 Dec 05, 2003 (119)
6 CSHL-HAPMAP ss16419553 Feb 27, 2004 (120)
7 CSHL-HAPMAP ss19849548 Feb 27, 2004 (120)
8 SSAHASNP ss20577626 Apr 05, 2004 (121)
9 ABI ss41189316 Mar 15, 2006 (126)
10 HGSV ss77596697 Dec 06, 2007 (129)
11 HGSV ss85572502 Dec 15, 2007 (130)
12 HUMANGENOME_JCVI ss97915491 Feb 06, 2009 (130)
13 BGI ss105114938 Dec 01, 2009 (131)
14 1000GENOMES ss109967513 Jan 24, 2009 (130)
15 ILLUMINA-UK ss118453526 Feb 14, 2009 (130)
16 ENSEMBL ss138971467 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss163004875 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss163738163 Jul 04, 2010 (132)
19 BUSHMAN ss197925092 Jul 04, 2010 (132)
20 BCM-HGSC-SUB ss205289571 Jul 04, 2010 (132)
21 1000GENOMES ss218203280 Jul 14, 2010 (132)
22 1000GENOMES ss230404165 Jul 14, 2010 (132)
23 1000GENOMES ss238123046 Jul 15, 2010 (132)
24 BL ss252880431 May 09, 2011 (134)
25 GMI ss275691463 May 04, 2012 (137)
26 GMI ss283991018 Apr 25, 2013 (138)
27 PJP ss290498327 May 09, 2011 (134)
28 TISHKOFF ss553734712 Apr 25, 2013 (138)
29 SSMP ss647536505 Apr 25, 2013 (138)
30 EVA-GONL ss974796513 Aug 21, 2014 (142)
31 JMKIDD_LAB ss1067627332 Aug 21, 2014 (142)
32 1000GENOMES ss1289451881 Aug 21, 2014 (142)
33 DDI ss1425693026 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1599427465 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1642421498 Apr 01, 2015 (144)
36 HAMMER_LAB ss1793785149 Sep 08, 2015 (146)
37 WEILL_CORNELL_DGM ss1917992037 Feb 12, 2016 (147)
38 GENOMED ss1966671389 Jul 19, 2016 (147)
39 JJLAB ss2019512171 Sep 14, 2016 (149)
40 USC_VALOUEV ss2147502551 Dec 20, 2016 (150)
41 HUMAN_LONGEVITY ss2159575035 Dec 20, 2016 (150)
42 TOPMED ss2321729974 Dec 20, 2016 (150)
43 SYSTEMSBIOZJU ss2624271844 Nov 08, 2017 (151)
44 GRF ss2697396586 Nov 08, 2017 (151)
45 GNOMAD ss2750972833 Nov 08, 2017 (151)
46 SWEGEN ss2986201407 Nov 08, 2017 (151)
47 BIOINF_KMB_FNS_UNIBA ss3023519707 Nov 08, 2017 (151)
48 TOPMED ss3067127661 Nov 08, 2017 (151)
49 CSHL ss3343288973 Nov 08, 2017 (151)
50 URBANLAB ss3646586766 Oct 11, 2018 (152)
51 EGCUT_WGS ss3654302630 Jul 12, 2019 (153)
52 EVA_DECODE ss3686047305 Jul 12, 2019 (153)
53 ACPOP ss3726740090 Jul 12, 2019 (153)
54 EVA ss3745755401 Jul 12, 2019 (153)
55 PACBIO ss3783308799 Jul 12, 2019 (153)
56 PACBIO ss3788985680 Jul 12, 2019 (153)
57 PACBIO ss3793858310 Jul 12, 2019 (153)
58 KHV_HUMAN_GENOMES ss3798777076 Jul 12, 2019 (153)
59 EVA ss3825993996 Apr 25, 2020 (154)
60 EVA ss3836384177 Apr 25, 2020 (154)
61 EVA ss3841788341 Apr 25, 2020 (154)
62 SGDP_PRJ ss3848069620 Apr 25, 2020 (154)
63 KRGDB ss3892931212 Apr 25, 2020 (154)
64 TOPMED ss4437306938 Apr 25, 2021 (155)
65 TOMMO_GENOMICS ss5142201894 Apr 25, 2021 (155)
66 1000Genomes NC_000001.10 - 3734447 Oct 11, 2018 (152)
67 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3734447 Oct 11, 2018 (152)
68 Genetic variation in the Estonian population NC_000001.10 - 3734447 Oct 11, 2018 (152)
69 gnomAD - Genomes NC_000001.11 - 3817883 Apr 25, 2021 (155)
70 Genome of the Netherlands Release 5 NC_000001.10 - 3734447 Apr 25, 2020 (154)
71 KOREAN population from KRGDB NC_000001.10 - 3734447 Apr 25, 2020 (154)
72 Northern Sweden NC_000001.10 - 3734447 Jul 12, 2019 (153)
73 Qatari NC_000001.10 - 3734447 Apr 25, 2020 (154)
74 SGDP_PRJ NC_000001.10 - 3734447 Apr 25, 2020 (154)
75 Siberian NC_000001.10 - 3734447 Apr 25, 2020 (154)
76 8.3KJPN NC_000001.10 - 3734447 Apr 25, 2021 (155)
77 TopMed NC_000001.11 - 3817883 Apr 25, 2021 (155)
78 UK 10K study - Twins NC_000001.10 - 3734447 Oct 11, 2018 (152)
79 A Vietnamese Genetic Variation Database NC_000001.10 - 3734447 Jul 12, 2019 (153)
80 ALFA NC_000001.11 - 3817883 Apr 25, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID History Updated (Build)
rs60999093 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77596697, ss85572502 NC_000001.8:3757603:G:A NC_000001.11:3817882:G:A (self)
ss109967513, ss118453526, ss163004875, ss163738163, ss197925092, ss205289571, ss252880431, ss275691463, ss283991018, ss290498327 NC_000001.9:3724306:G:A NC_000001.11:3817882:G:A (self)
119911, 53710, 40878, 23119, 108606, 24955, 33967, 86600, 18905, 171201, 53710, 11358, ss218203280, ss230404165, ss238123046, ss553734712, ss647536505, ss974796513, ss1067627332, ss1289451881, ss1425693026, ss1599427465, ss1642421498, ss1793785149, ss1917992037, ss1966671389, ss2019512171, ss2147502551, ss2321729974, ss2624271844, ss2697396586, ss2750972833, ss2986201407, ss3343288973, ss3654302630, ss3726740090, ss3745755401, ss3783308799, ss3788985680, ss3793858310, ss3825993996, ss3836384177, ss3848069620, ss3892931212, ss5142201894 NC_000001.10:3734446:G:A NC_000001.11:3817882:G:A (self)
864761, 568575, 913273, 1649328710, ss2159575035, ss3023519707, ss3067127661, ss3646586766, ss3686047305, ss3798777076, ss3841788341, ss4437306938 NC_000001.11:3817882:G:A NC_000001.11:3817882:G:A (self)
ss9897076, ss12992576, ss16419553, ss19849548, ss20577626 NT_004321.15:1041220:G:A NC_000001.11:3817882:G:A (self)
ss1289624, ss5894393, ss6396329, ss41189316, ss97915491, ss105114938, ss138971467 NT_004350.19:3213078:G:A NC_000001.11:3817882:G:A (self)
108606, ss3892931212 NC_000001.10:3734446:G:C NC_000001.11:3817882:G:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1104856

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post596+ae089ad